Varga_2019_NEE_PhyloBayes_FastDate.zip (6.11 MB)

Input files and the results of the molecular clock analysis (PhyloBayes & FastDate) of the 5,284 taxa data set

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posted on 24.11.2019 by Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, Marisol Sánchez-García, Santiago Sánchez-Ramírez, Gergely J. Szöllősi, János G. Szarkándi, Viktor Papp, László Albert, William Andreopoulos, Claudio Angelini, Vladimír Antonín, Kerrie W. Barry, Neale L. Bougher, Peter Buchanan, Bart Buyck, Viktória Bense, Pam Catcheside, Mansi Chovatia, Jerry Cooper, Wolfgang Dämon, Dennis Desjardin, Péter Finy, József Geml, Sajeet Haridas, Karen Hughes, Alfredo F. Justo, Dariusz Karasiński, Ivona Kautmanova, Brigitta Kiss, Sándor Kocsubé, Heikki Kotiranta, Kurt M. LaButti, Bernardo E. Lechner, Kare Liimatainen, Anna Lipzen, Zoltán Lukács, Sirma Mihaltcheva, Louis Morgado, Tuula Niskanen, Machiel E. Noordeloos, Robin A. Ohm, Beatriz Ortiz-Santana, Clark Ovrebo, Nikolett Rácz, Robert Riley, Anton Savchenko, Anton Shiryaev, Karl Soop, Viacheslav Spirin, Csilla Szebenyi, Michal Tomšovský, Rodham E. Tulloss, Jessie Uehling, Igor V. Grigoriev, Csaba Vágvölgyi, Tamás Papp, Francis M. Martin, Otto Miettinen, David S. Hibbett, László G. Nagy
There are three sub-directories: PhyloBayes_input, PhyloBayes_output and FastDate_analysis. The whole analysis started with PhyloBayes. The PhyloBayes input files are the following. fb_align_*.phy: 10 alignments, containing 543 taxa after randomly deleted the ~90% of the tips from the 5284taxa dataset. fb_calib_*.cal: 10 files, containing species pairs which define the constrains on the MRCA. fb_tree_*.tre: 10 phylogenies, containing 543 taxa after randomly deleted the ~90% of the tips from the 5284taxa dataset. PhyloBayes analyses were run using the 10% subsampled dataset, a birth-death prior on divergence times, an uncorrelated gamma multiplier relaxed clock model and a CAT-poisson substitution model with a gamma distribution on the rate across sites. A uniformly distributed prior was applied to fossil calibration times. All analyses were run until convergence, typically 15,000 cycles. Convergence of chains was assessed by visually inspecting the likelihood values of the trees and the tree height parameter. We sampled every tree from the posterior and after discarding the first 7,000 samples as burn-in we summarized the posterior estimates using the readdiv function of PhyloBayes. The results can be found in the PhyloBayes_output directory. The directory FastDate_anaysis contains the input files. calib_final_tree_*_.cal: 10 files, containing species pairs which define the constrains on the MRCA. FastDate was run on the complete trees (5,284 species) with the node ages constrained to the values of the 95% highest posterior densities of the ages inferred by PhyloBayes. tree_original_*.tree2: 10 phylogenies, containing 5284 taxa. These trees came from the 5284taxa ML analysis. FastDate analyses were run with time discretized into 1,000 intervals and the ratio of sampled extant individuals set to 0.14. The output files are the followings. fastdate_kronogram_*.tree: 10 chronograms inferred by FastDate analysis. transform_to_ultrametric_script.R: An R script which transforms trees to ultrametric. Because rounding issues, a negligible length was added to some of the tips to achieve ultrametric trees. fastdate_kronogram_*.tree2: 10 chronograms used in further analysis.

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dc.type.embargo

none

dc.format.extent

6406597

dc.identifier.uri

http://hdl.handle.net/10255/dryad.203720

dc.coverage.spatial

World wide

dc.coverage.temporal

Mesozoic era, Cenozoic era

dwc.ScientificName

Agaricomycetes

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